consensus.seqs summary file change

diff --git a/consensusseqscommand.cpp b/consensusseqscommand.cpp
index 9c447c217b30247bedbddb7b3351b71952de4c55..513566f0c4fd75990f781e2b4a482332cfe5ac12 100644 (file)
--- a/consensusseqscommand.cpp
+++ b/consensusseqscommand.cpp
@@ -203,6 +203,8 @@ int ConsensusSeqsCommand::execute(){
                        outSummary.setf(ios::fixed, ios::floatfield); outSummary.setf(ios::showpoint);
                        outputNames.push_back(outputSummaryFile); outputTypes["summary"].push_back(outputSummaryFile);
                        
+                       outSummary << "PositioninAlignment\tA\tT\tG\tC\tGap\tNumberofSeqs\tConsensusBase" << endl;
+                       
                        ofstream outFasta;
                        string outputFastaFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "cons.fasta";
                        m->openOutputFile(outputFastaFile, outFasta);
@@ -259,21 +261,9 @@ int ConsensusSeqsCommand::execute(){
                                
                        }
                        
-                       outSummary << "A" << '\t';
-                       for (int j = 0; j < seqLength; j++) { outSummary << percentages[0][j] << '\t'; }
-                       outSummary << endl;
-                       outSummary << "T" << '\t';
-                       for (int j = 0; j < seqLength; j++) { outSummary << percentages[1][j] << '\t'; }
-                       outSummary << endl;
-                       outSummary << "G" << '\t';
-                       for (int j = 0; j < seqLength; j++) { outSummary << percentages[2][j] << '\t'; }
-                       outSummary << endl;
-                       outSummary << "C" << '\t';
-                       for (int j = 0; j < seqLength; j++) { outSummary << percentages[3][j] << '\t'; }
-                       outSummary << endl;
-                       outSummary << "Gap" << '\t';
-                       for (int j = 0; j < seqLength; j++) { outSummary << percentages[4][j] << '\t'; }
-                       outSummary << endl;
+                       for (int j = 0; j < seqLength; j++) { 
+                               outSummary << (j+1) << '\t' << percentages[0][j] << '\t'<< percentages[1][j] << '\t'<< percentages[2][j] << '\t' << percentages[3][j] << '\t' << percentages[4][j] << '\t' << seqs.size() << '\t' << consSeq[j] << endl;
+                       }
                        
                                
                        outFasta << ">conseq" << endl << consSeq << endl;
@@ -399,6 +389,8 @@ int ConsensusSeqsCommand::processList(ListVector*& list){
                m->openOutputFile(outputFastaFile, outFasta);
                outputNames.push_back(outputFastaFile); outputTypes["fasta"].push_back(outputFastaFile);
                
+               outSummary << "OTU#\tPositioninAlignment\tA\tT\tG\tC\tGap\tNumberofSeqs\tConsensusBase" << endl;
+               
                for (int i = 0; i < list->getNumBins(); i++) {
                        
                        if (m->control_pressed) { outSummary.close(); outName.close(); outFasta.close(); return 0; }
@@ -512,23 +504,9 @@ string ConsensusSeqsCommand::getConsSeq(string bin, ofstream& outSummary, string
                        
                }
                
-               outSummary << ">seq" << (binNumber + 1) << endl;
-               outSummary << "A" << '\t';
-               for (int j = 0; j < seqLength; j++) { outSummary << percentages[0][j] << '\t'; }
-               outSummary << endl;
-               outSummary << "T" << '\t';
-               for (int j = 0; j < seqLength; j++) { outSummary << percentages[1][j] << '\t'; }
-               outSummary << endl;
-               outSummary << "G" << '\t';
-               for (int j = 0; j < seqLength; j++) { outSummary << percentages[2][j] << '\t'; }
-               outSummary << endl;
-               outSummary << "C" << '\t';
-               for (int j = 0; j < seqLength; j++) { outSummary << percentages[3][j] << '\t'; }
-               outSummary << endl;
-               outSummary << "Gap" << '\t';
-               for (int j = 0; j < seqLength; j++) { outSummary << percentages[4][j] << '\t'; }
-               outSummary << endl;
-               
+               for (int j = 0; j < seqLength; j++) { 
+                       outSummary << (binNumber + 1) << '\t' << (j+1) << '\t' << percentages[0][j] << '\t'<< percentages[1][j] << '\t'<< percentages[2][j] << '\t' << percentages[3][j] << '\t' << percentages[4][j] << '\t' << seqs.size() << '\t' << consSeq[j] << endl;
+               }
                
                return consSeq;
                

diff --git a/mothur b/mothur
index 0f23015f75ecfda6bb2b8573acf2502237933abc..3b721adfb6d23378be97bdbf2e494d296d3406ff 100755 (executable)
Binary files a/mothur and b/mothur differ